Communities in the vicinity of the Mico River, located in Chontales, Nicaragua, suffer from periodic dry season water shortages. The Mico River is impacted by artisanal and industrial mining, cattle ranching, effluent from local dairies and tanneries, and poor waste management practices in the watershed. Available water quality data consists of short term assessment studies and monitoring data for a mine operating in the headwaters, but to date this information has not been collated and interpreted as a whole. Communities in the vicinity of the Mico River have expressed an interest in having this data reviewed to verify information they have received from government and industry with regards to impacts from the La Libertad Mine. A gap analysis of existing water quality data in the headwaters of the Mico River is presented, with interpretation of current data and identification of further data needs. Recommendations are provided for future water quality monitoring in the region. The study area was defined as the Mico River watershed upstream of the town of Santo Tomas. A total of 14 studies were identified with information about the Mico River in this area. Individual study reliability was assessed, and study data were compiled to assess conditions in comparison to water quality guidelines and any spatial or temporal trends. Both water chemistry and bioassessment studies were assessed. The major gaps in existing information are: insufficient baseline/ reference information, insufficient information on impacts from contaminants other than metals, insufficient coverage of streams not directly impacted by the La Libertad Mine, poor quality and reliability of data, and poor coordination/ continuity between studies done to date. Cyanide concentrations were found to be below drinking water criteria at the majority of sample locations. Metals concentrations were elevated throughout the study area but it cannot be determined if this is due to natural background levels or anthropogenic sources. Water quality conditions with regards to other parameters (e.g., dissolved oxygen, temperature, pesticides and bacteria) and bioassessment data cannot be assessed due insufficient data quality and quantity. Existing monitoring in the region should be expanded to include reference locations. It is recommended that a benthic invertebrate bioassessment program designed for tropical mountain streams be implemented to supplement existing monitoring and identify areas where stream function is impaired, as bioassessment is cheaper and requires less equipment and logistical coordination than water chemistry monitoring programs. Whatever future work is done, care must be taken that study design and implementation is of a higher quality than that done to date, so that results are comparable and reliable. Coordination and cooperation between bodies involved in monitoring is essential for efficient use of scarce resources. / Graduate

Les diatomées sont des microalgues ubiquistes d'une diversité exceptionnelle. Cela en fait de bons indicateurs de la qualité des écosystèmes aquatiques et sont utilisées depuis plus de 50 ans. Depuis l'année 2000, la Directive Cadre Européenne sur l'Eau impose leur utilisation pour évaluer la qualité écologique des cours d'eau. Un cadre typologique doit être utilisé afin de comparer des rivières comparables entre elles, c'est-à-dire des rivières de mêmes régions bioclimatiques, coulant sur les mêmes substrats géologiques et à des altitudes comparables. Différentes classifications écorégionales ont été définies sur la base de ces paramètres. Nous avons montré qu'à une échelle couvrant 4 pays (Espagne, France, Italie, Suisse) et à une régionale (Nord-est de la France), les écorégions et la géologie sont déterminantes pour expliquer les communautés. Les paramètres caractérisant la pollution sont moins importants. Contrairement à certains auteurs, nous n'avons pas observé d'homogénéisation des communautés lorsque le niveau de pollution augmente. D'autre part nous n'avons pas observé de communautés restreintes géographiquement : cela permettrait de rassembler des écorégions distinctes géographiquement mais présentant les mêmes caractéristiques physiques. Les diatomées présentent une diversité spécifique très importante qui peut être un frein à leur utilisation en routine. Nous avons montré qu'en augmentant la précision de détermination (de la subdivision à l'espèce), les performances d'évaluation de la pollution augmentait mais beaucoup moins que le nombre de taxons. Les performances d'évaluation entre le genre et l'espèce sont d'ailleurs proches, alors qu'il y a dix fois plus d'espèce que de genres. Nous avons montré aussi que des métriques simplificatrices (formes de vie, guildes écologiques) permettaient d'évaluer aussi bien le niveau en nutriment que des indices diatomiques basés sur les espèces. Ces métriques apportent des informations supplémentaires en termes de structure de biofilm qui ne sont accessible aux données en espèce. Enfin, la pollution des rivières par les micropolluants devient une préoccupation sociétale croissante. Nous avons émis l'hypothèse que les diatomées pouvaient être de bons candidats pour évaluer la pression en herbicides. Quatre expérimentations de 2 mois ont été réalisées en mésocosmes lotiques. Nous avons montré que les diatomées vivant entourées de matrices polysaccharidiques épaisses étaient plus résistantes aux pesticides dissous. Au contraire les diatomées présentant une surface cellulaire de contact importante avec l'eau étaient défavorisées. Ce type de métrique pourrait être utilisé in situ à plus large échelle. Nous concluons sur l'intérêt d'intégrer ces métriques à la bioindication par les diatomées. Mais également nous soulignons l'importance de croiser la phylogénie et l'écologie pour mieux comprendre quelles pressions environnementales ont forcées les diatomées à s'adapter. Si ces pressions peuvent être reliées à des pressions anthropiques, la bioindication par les diatomées en sera améliorée. / Diatoms are ubiquitous microalgae of an extreme diversity. This made them good indicators of aquatic ecosystems quality and they are used since 50 years for this purpose. Since year 2000, the European Water Framework Directive requires their use to assess the ecological quality of watercourses. A typological framework has to be used in order to compare comparable rivers between each other, that is, rivers of the same bioclimatic regions, flowing on the same geological substrate at similar altitudes. Various ecoregional classifications were defined on the basis of these parameters. We showed at a scale covering 4 countries (Spain, France, Italy and Switzerland) and at a regional scale (north-east France) that ecoregions and geology are determinant to explain communities. Parameters characterizing pollution were less important. Unlike some authors, we did not observe any homogenization of the communities when pollution level was increasing. Moreover, we did not observe geographically restricted communities: this would enable to aggregate ecoregions geographically distinct but presenting the same physical characteristics. Diatoms display a very important specific diversity which can be a problem for their routine use. We showed that when increasing determination precision (from sub-division to species), pollution assessment performances were increasing but much less than the number of taxa. Assessment performances between genus and species are similar anyway, whereas there are ten time more species than genera. We also showed that using simplifying metrics (life-forms, ecological guilds) enable assessing nutrient level as well as diatom indices based on species. These metrics bring additional information about biofilms structure that is not available with species data. At last, micropollutants pollution in rivers is of increasing concern to citizens. We hypothesized that diatoms could be good candidates to assess herbicide pressure. Four experiments lasting 2 months were conducted in lotic mesocosms. We showed that diatoms surrounded by thick exopolysaccharid matrices were more resistant to dissolved pesticides. On the over hand, diatoms presenting an important cell surface contact with water were disadvantaged. This kind of metric could be used in situ at a larger scale. We conclude on the interest to integrate such metrics to diatom bioassessment. But we also strength the importance to cross phylogeny and ecology to better understand which environmental pressure forced diatoms adapt. If these pressures can be related to anthropogenic pressures, diatom bioassessment will be improved.

ABSTRACT A review of annual monitoring reports for stream restoration projects on surface coal mines in the central Appalachian Mountains found that the criteria used for judging the success of the projects was generally based on visual assessments of habitat structure which were evaluated using the Rapid Bioassessment Protocol (RBP) (Palmer and Hondula, 2014). In recent years the Hydrogeomorphic Approach (HGM), which was originally developed to evaluate wetlands, has been adapted for stream evaluations as well (Summers, et al., 2017). Both of these methods are primarily a means to determine if suitable habitat structure and riparian growth are present to support aquatic life. It is assumed that if habitat structure is suitable then macroinvertebrate and other life will be present. However, each of these two methods place emphasis on different aspects of habitat and riparian structure. The primary purpose of this project is to compare and contrast how effective these two methods are at evaluating reconstructed streams on surface coal mines. A secondary objective is to determine if macroinvertebrate assemblages in reconstructed streams is significantly different from that of reference streams not impacted by mining. Research on benthic community structure downstream of coal mining activities suggests that even after many decades taxa richness and abundance still have not recovered from indirect impacts (Petty, et al., 2010). Information on reconstructed streams directly impacted is lacking. This project evaluates streams that were reconstructed five years prior using the RBP and HGM methods, and compares them to local reference streams that have minimal to no mining impacts. Multiple benthic metrics are also used to evaluate community structure. REFERENCES Petty, J. Todd, Jennifer B. Fulton, Michael P. Strager, George T. Merovich Jr., James M. Stiles, and Paul F. Ziemkiewicz. 2010. Lanscape indicators and thresholds of stream ecological impairment in an intensely mined Appalachian watershed. Journal of the North American Benthological Society, 29(4): 1292-1309. Palmer, Margaret A., and Kelly L. Hondula. 2014. Restoration as mitigation: analysis of stream mitigation for coal mining impacts in southern Appalachia. Environmental Science and Technology 48: 10552-10560. Summers, Elizabeth A., Chris V. Noble, Jacob F. berkowitz, and Frank J. Spilker. 2017. Operational Draft Regional Guidebook for the Functional Assessment of High-Gradient Headwater Streams and Low-Gradient Perennial Streams in Appalachia. ERDC/EL TR-17-1.

Degraded rivers and streams caused by disturbances have created a need for reliable tools to assess the ecological status of such ecosystems. Numerous methods and programs have been developed to assess ecological status using biological indicators, benthic macroinvertebrates are the most commonly used biotic indicator. The Hester-Dendy multi-plate sampler is a commonly used tool for sampling benthic macroinvertebrates, but its effectiveness under different environmental conditions has not been adequately tested. The aim of this study was to investigate if HD samplers assess the benthic macroinvertebrate community equally under different flow conditions. I investigated if the colonization of BMI in a constant flow differed from that of a variable flow (simulating a hydropeaking flow regime). This was studied using six aquariums, three as control with constant flows and three with variable flow conditions. One Hester-Dendy sampler and 50 benthic macro invertebrates from five different taxonomic orders were place in each aquarium. After five days of colonization the Hester-Dendy samplers were retrieved and benthic macroinvertebrates colonizing the Hester-Dendy samplers and still remaining in the aquariums were collected, preserved and analysed. Results showed that the mean sampling efficiency did not differ between the two treatments. On the other hand species diversity calculated from Shannon-Wiener index was significantly higher in the control treatment than in the variable flow treatment. The lower species diversity in the variable flow treatment is consistent with previous research on benthic macroinvertebrates affected by hydropeaking powerplants. These results can be seen as an indication of how a variable flow regime might affect the samples collected by HD samplers in a natural environment. As the artificial environments created are greatly different from a natural environment, this result might not therefore be representative in a natural environment. / Vattendrag kraftigt påverkade av antropogena störningarna har skapat ett behov av tillförlitliga verktyg för att kunna bedöma dessa vattendrags ekologiska status. Många olika metoder och program har utvecklats genom att använda olika biologiska indikatorer. Bentiska makroevertebrater är en av de vanligaste biotiska indikatorerna. En vanlig metod för att prov ta bentiska makroevertebrater är Hester-Dendy provtagaren. Syftet med denna studie var således att testa om provtagningseffektiviteten för Hester-Dendy provtagare påverkas olika av ett variabelt vattenflöde jämfört med ett jämnt vattenflöde. Detta studerades i sex akvarium, där tre akvarium agerade kontroll och utsattes för ett jämt flöde samt tre akvarium med variabelt flöde. En Hester-Dendy provtagare och 50 bentiska makroevertebrater från fem olika taxonomiska ordningar placerades i varje akvarium. Efter fem dagars koloniserings tid hämtades Hester-Dendy provtagarna och de bentiska makroevertebrater som koloniserade provtagaren såväl som akvariet bevarades i etanol och analyserades i labbet. Resultaten visade att den genomsnittliga provtagningseffektiviteten inte skilde sig åt mellan de två behandlingarna. Däremot var artdiversiteten beräknad med Shannon-Wiener-index signifikant högre i kontrollbehandlingen. Den lägre artdiversiteten i behandlingen med variabelt flöde stämmer överens med tidigare forskning om bentiska makroevertebrater påverkade av korttidsreglerande vattenkraftverk. Resultaten i denna studie bör ses som en indikation av hur ett varierande flöde kan påverka provtagnings effektiviteten hos en Hester-Dendy-provtagare. Detta med anledning av att den konstgjorda miljön som försöket utfördes i är vitt skilt från organismernas naturliga miljö vilket kan ha påverkat resultatet.

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This post-fire study was conducted to characterize and observe fire induced changes in physical habitat parameters, water-quality conditions and macroinvertebrate assemblages in the Little Creek watershed, a tributary to Scotts Creek located in Cal Poly’s Swanton Pacific Ranch in Davenport, California. Pre-fire data was collected by a Cal Poly student, John Hardy, for his 2017 thesis. Post-burn bioassessment surveys for this study were repeated at four of the same study sites used by Hardy to provide comparisons to the California Stream Condition Index via a modified version of the State of California’s Surface Water Ambient Monitoring Program protocol. Macroinvertebrates were taxonomically identified to the family level. Commonly used bioassessment indices were utilized in conjunction with Stepwise regression and Analysis of Variance on both pre- and post-fire datasets to illustrate how physical habitat and water quality parameters changed after the fire and to determine the significance of collected environmental variables (stream shading, cross sectional area, and median particle size) as predictors of macroinvertebrate community structure. Despite most of Little Creek having moderate and high burn severities, it was found that physical habitat, water quality and benthic macroinvertebrate populations were not greatly disturbed by the 2020 CZU lighting complex fire. Proportions of highly disturbance/pollution sensitive taxa and increased following the wildfire and there was a dramatic shift from collector-gatherer to predator organisms. Comparison of pre- and post-fire data in this study showed fire having a minimal effect on the studied watershed. Difference in study goals and associated protocols used in the pre- and post-fire studies and the low water year following the wildfire, complicates statistical comparisons and poses threat to the validity of results. However, there is opportunity for further investigation about the ability of an ecosystem to successfully recover from natural disasters and disturbances, specifically when there is little human impact (or influence) on the ecosystem.

Stream fish assemblages exist within stream networks defined by the size and proximity of connected streams (i.e., stream network topology). The spatial position of sites within stream networks may therefore regulate opportunities for fish dispersal to access distant resources or colonize "new" habitats. Such inter-stream dispersal dynamics will influence local fish assemblage structure and the vulnerability of local assemblages to anthropogenic stressors. In this dissertation, I explored the effects of stream network topology on fish assemblage structure in the mid-Atlantic highlands, USA and tested the hypothesis that dispersal would affect the sensitivity of fish-based environmental quality assessments (i.e., bioassessments). In chapter 1, I evaluated the effects of stream networks by comparing fish assemblages between sites with and without large downstream confluences (>3rd order) in western Virginia, USA (i.e., mainstem tributaries and headwater tributaries, respectively). I found that local species richness was higher in mainstem tributaries than headwater tributaries and that these effects could not be explained by variation in local environmental habitat conditions. In chapter 2, I developed and applied a continuous model of stream network topology to explore the effects of downstream size and proximity on local fish assemblage structure within the mid-Atlantic highlands. I found that fish assemblage structure (i.e., Bray-Curtis distances in species abundance) was significantly related to variation in stream network topology up to approximately 9 fluvial km from sites. Chapters 3 and 4 explored the implications of inter-stream dispersal for fish bioassessments. In Chapter 3, I identified 10 fish metrics that corresponded predictably to environmental stressors in the mid-Atlantic highlands. However, headwater tributary assemblages showed stronger relations to local environmental quality than mainstem tributaries, consistent with the hypothesis of riverine dispersal. In Chapter 4, I compared the effects of stream network topology on fish and benthic macroinvertebrate assemblages. Fish metrics were influenced by the size and proximity of connected streams but benthic macroinvertebrate metrics were not. This finding suggests that stream fishes may complement benthic macroinvertebrate bioassessments by indicating environmental conditions at larger spatial grains. / Ph. D.

Traits provide an informative approach to examine species-environment interactions. Often, species-by-species approaches are inefficient to generate generalizable ecological relationships and do not predict species responses to environmental changes based on specific traits species possess. Multiple lines of inquiry and multi-scale approaches are best for assessing environment-trait responses. This thesis examines important questions not specifically addressed before in traits-based research. Chapter one explores biological and ecological trait associations incorporating ontogenetic diet shifts for New River fishes. Niche shift analysis as a chapter one sub-objective quantitatively support where species-specific diet shifts likely occur. Strong biological-ecological trait associations, some intuitive and others not so intuitive, were found that relate biological structure to ecological function. Improved understanding of trait associations, including what factors influence others, supports inference of ecology of fishes. Chapters two and three examine spatial and intraspecific trait variability. Chapter two specifically examines large-scale life history trait variability along latitudinal gradients for twelve widely distributed fish species, including directionality of trait variation, and hypothesizing how optimal traits change with large-scale environmental factors. Strong positive and negative patterns found include average total length of newly hatched larvae, average total length at maturation, average spawning temperature, average egg diameter, and maximum length. These five traits are correlated with other adaptive attributes (i.e. growth rate, reproductive output, and longevity/population turnover rate). In contrast to latitudinal scale, Chapter three examines trait variability of white sucker (Catostomus commersonii) and fantail darter (Etheostoma flabellare) as a function of small-watershed scale spatial factors and anthropogenic disturbance. Toms Creek and Chestnut Creek white sucker and fantail darter displayed positive response to disturbance, contrary to past studies. Lower resource competition, and / or competitive exclusion of fishes with similar niche requirements are possible mechanisms. All three objectives support understanding of trait association and variability as a useful foundation in ecological applications and for formulating plans for conservation and management of species. / Master of Science

The river drainages originating in the Cumberland region of Virginia, Tennessee and Kentucky are home to some of the last surviving and most diverse assemblages of native freshwater mussels. This region of the country also has historically and continues to be a major source of coal for the United States. Numerous experiments were carried out in an attempt to determine what ecotoxicological effects these activities have had on mussels as well as what has been done to correct some of the most severe cases of environmental pollution due to historical coal mining operations. Analysis of interstitial water (IW), sediment and in situ toxicity testing and chemical analyses showed that the most likely cause for mussel declines was elevated metal concentrations (Al, Cu, Fe, Pb) found in IW. Ecotoxicological assessments of the two streams (Black and Ely Creeks) most impacted by acid mine drainage (AMD) in the state of Virginia were carried out to determine their potential for future degradation of the Powell River watershed into which they drain. The Powell River is a major system still inhabited by native mussels. Sophisticated wetland systems built at Ely Creek have significantly improved the ecological health of Ely Creek, decreasing the pollution into the Powell River. Reclamation and wetland construction at Black Creek have had a positive impact but active coal mining and un-remediated AMD are still negatively affecting this system. After the watershed has been fully reclaimed the discharge from Black Creek will likely be improved. / Master of Science

The Bonneville Basin encompasses an area that was covered by ancient Lake Bonneville and which today lies within the Great Basin province. The Bonneville Basin is distinguished geologically by its characteristic parallel north-south mountain ranges that are separated by broad, alluviated desert basins and valleys. Benches and other shoreline features of ancient Lake Bonneville prominently mark the steep, gravelly slopes of these ranges. Numerous artesian desert springs are present at the base of the mountains and in the valley floors that form various sizes of both isolated wetlands and wetland complexes. Many these wetlands are some of the most unique and currently some of the most threatened wetlands in the United States. Several aquatic species and communities have maintained an existence as relict populations and communities in these wetlands since the receding of Lake Bonneville over 10,000 years ago. For example, Hershler has described 58 previously undescribed species of hydrobiid snails, 22 of which are endemic to single locations. Like hydrobiid snails, numerous other species, such as the least chub, Iotichthys phlegethontis and the Columbia spotted frog, Rana luteioventris, depend on these wetlands for their continued existence, many of which are already imperiled. The continued decline and loss of these wetlands would further push many of these species toward endangerment and/or extinction. Several factors have already eliminated or altered many of these habitats including capping and filling,water depletions, agricultural practices, livestock grazing, and introduction of nonnative species. In recent years, the significant loss and degradation of wetlands resulting in sensitive species designations have provided impetus for resource agencies to develop and implement management plans to conserve and protect these vital ecosystems. One problem facing appropriate management is the lack of biological information for determining which wetlands should receive protection priorities based on the presence of viable, functioning characteristics. The purpose of this dissertation project was to obtain biological information needed to support defensible decisions concerning conservation, protection, acquisition, restoration, and mitigation of the artesian springs in the Bonneville Basin. The primary objectives of this project were to 1) Develop bioassessment procedures for artesian wetlands of the Bonneville Basin using macroinvertebrates and 2) Determine patterns of community composition and diversity for macroinvertebrates and metaphyton algae at multiple scales in Bonneville Basin artesian wetlands.